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- PDB-3sax: Crystal structure of human carbonic anhydrase isozyme II with 2-c... -

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Basic information

Entry
Database: PDB / ID: 3sax
TitleCrystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-{[(5-ethyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / drug design / sulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-E50 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.1 Å
AuthorsGrazulis, S. / Manakova, E. / Tamulaitiene, G.
CitationJournal: Eur.J.Med.Chem. / Year: 2012
Title: Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases.
Authors: Capkauskaite, E. / Zubriene, A. / Baranauskiene, L. / Tamulaitiene, G. / Manakova, E. / Kairys, V. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0466
Polymers29,2891
Non-polymers7575
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.221, 41.172, 72.197
Angle α, β, γ (deg.)90.000, 104.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 361 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E50 / 2-chloro-5-{[(5-ethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide


Mass: 371.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClN3O3S2
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Na-bicine pH 9, 2.6M Na-malonate pH 7.55, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2010 / Details: Mirror Bent, vertically focussing
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.1→41.172 Å / Num. obs: 92709 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 7.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.1-1.155.50.2752.663186114030.27579.2
1.15-1.2260.2123.376210128050.21293.6
1.22-1.3160.1664.372146120970.16694.4
1.31-1.4160.1285.567672113480.12894.9
1.41-1.5560.0957.163028105680.09595.9
1.55-1.7360.0729.15737096310.07296.5
1.73-25.90.05611.35088285620.05697.2
2-2.4413.60.0947.29963273430.09497.8
2.44-3.4613.80.0610.97917157230.0698.6
3.46-41.1712.20.0511.93930832290.0598.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.3.16data scaling
PDB_EXTRACT3.006data extraction
DNAdata collection
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3HLJ

3hlj


Resolution: 1.1→35.49 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.128 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.93 / SU R Cruickshank DPI: 0.035 / SU Rfree: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 9255 10 %RANDOM
Rwork0.126 ---
all0.129 92668 --
obs0.129 92668 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.87 Å2 / Biso mean: 12.365 Å2 / Biso min: 3.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.06 Å2
2--0.3 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.1→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 43 356 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222904
X-RAY DIFFRACTIONr_bond_other_d00.021959
X-RAY DIFFRACTIONr_angle_refined_deg2.5241.9673965
X-RAY DIFFRACTIONr_angle_other_deg4.32534819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02925.188133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37515481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.752158
X-RAY DIFFRACTIONr_chiral_restr0.1530.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023320
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02571
X-RAY DIFFRACTIONr_nbd_refined0.2760.2487
X-RAY DIFFRACTIONr_nbd_other0.2580.21566
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21091
X-RAY DIFFRACTIONr_nbtor_other0.1120.21017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2245
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.248
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.283
X-RAY DIFFRACTIONr_mcbond_it2.5221.51761
X-RAY DIFFRACTIONr_mcbond_other3.9681.5708
X-RAY DIFFRACTIONr_mcangle_it3.38222870
X-RAY DIFFRACTIONr_scbond_it4.37131143
X-RAY DIFFRACTIONr_scangle_it5.6794.51095
X-RAY DIFFRACTIONr_rigid_bond_restr3.27934863
X-RAY DIFFRACTIONr_sphericity_free15.3693378
X-RAY DIFFRACTIONr_sphericity_bonded5.80634771
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 628 -
Rwork0.197 5507 -
all-6135 -
obs--85.14 %

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